[gmx-users] PMF trails off to infinity.

Laura Kingsley lkingsle at purdue.edu
Mon Jul 2 15:54:06 CEST 2012


I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm.  As I pull the ligand from 3A toward 0 A, the PMF starts  a dramatic uphill climb. This does not agree with the force profile which seems to level out. Any ideas about what might be going wrong here? I am thinking this probably isn't correct, but I don't know where I've messed up. Thanks! I can attach the graphs if necessary.

- Laura

Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643

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